Ok, so I've done something extremely stupid. I blew up some stuff on my motherboard and now I've got a new one.
I migrated from a Gigabyte EX58-UD3R to a EX58-UD5 and I was using Gigabyte's onboard raid controller for a RAID-0 setup (not the ICH10R from Intel) with 2 500Gb harddisks.

Now I've built everything around the UD5, but I am kind of a n00b with RAID controllers. I plugged in the disks in the same order on Gigabyte's own controller again but no RAID as far as I can tell.
I'm holding back to reinitialise the array since it effectively holds everything that was on the computer, including over 200Gbs of music and I don't know if initialising means data loss.

UD3R's controller is a JMicron JMB363 and so is the UD5's.

If someone can point me to utilities, boot cd's or whatever I can use to double and triple check whether my data will still be there when I reinitialise the array I'd be very, very thankful

I enabled the raid controller itself. Then I went into the SmartBackup section, which basically allows me to "set" the raid level for the Jmicron controller. The big fat warning for data loss is holding me back to set it on raid-0 though (plus it's on 0 already).
I can try if this can be done without the disks present and then plug them in afterwards.

Tough situation. The exact reason why I stopped using Raid 0. I think Raid 0 does give some nice benefits, but my data is too important.

AFAIK, all your data is currently in tact. However I'm not sure what 'initialization' will include. If it just creates the RAID structure, you should be ok. (The current sturcture will simply be overwritten by the new one, leaving data in place) But 'initialization' could involve more than that which will put your data in jeopardy. But you prolly knew everything I just said.

I do have to ask, why did you pick the JMicron controller over the ICH10R?

Tough situation. The exact reason why I stopped using Raid 0. I think Raid 0 does give some nice benefits, but my data is too important.

AFAIK, all your data is currently in tact. However I'm not sure what 'initialization' will include. If it just creates the RAID structure, you should be ok. (The current sturcture will simply be overwritten by the new one, leaving data in place) But 'initialization' could involve more than that which will put your data in jeopardy. But you prolly knew everything I just said.

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What you say is exactly why I'm hesitating

I do have to ask, why did you pick the JMicron controller over the ICH10R?

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No particular reason really, guess I was thinking something in the likes of balancing the load between the chipsets.

I just got a tip from a colleague, gonna see if I can set some jumper or something on these disks to write-protect them and then initialise the RAID. Though a tool for checking which disk is which would still be very much welcomed.

Just move the disks to another board, and place them in a similar hierarchy (order of SATA port number). Set the controller to RAID mode, and see if the array gets listed in the RAID BIOS setup. I was able to migrate my RAID 0 intact between a motherboard with AMD SB600 to one with SB700.

Can you use something like Acronis Disk Director to image your drives for backup purpose in case it goes wrong? I dont know if that is possible, but just a thought.

Otherwise to be on the VERY SAFE side, I would suggest you pick up an identical mainboard off ebay. Get the drives booted. Save the critical data. Migrate. Resell the ebay board. Total loss: time and shipping costs and maybe a small trading loss. But it is the safest bet.

Can you use something like Acronis Disk Director to image your drives for backup purpose in case it goes wrong? I dont know if that is possible, but just a thought.

Otherwise to be on the VERY SAFE side, I would suggest you pick up an identical mainboard off ebay. Get the drives booted. Save the critical data. Migrate. Resell the ebay board. Total loss: time and shipping costs. But it is the safest bet.

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Even on an identical board I still need to plug in the drives in the correct way and initialise the RAID array I'm looking my ass off for a good tool, Acronis has helped me in the past with TrueImage though, I might take a look there as well.

I tried simply booting with the disks plugged in either way (so without RAID enabled).

One way gives me a "NON SYSTEM DISK" message
The other way gives me a "Read error" message

My hunch is that the NON SYSTEM DISK message is caused by an incorrect order since it can't find an MBR and the "Read error" tells me that it found an MBR record but cannot read the next bits correctly since RAID isn't configured.

first of all it doesn't matter what order the disks are in. second, all you should have to do is enable RAID in the BIOS for the proper SATA ports, save and reboot and when the intel RAID screen comes up it should detect the RAID array. the only time this has not worked for me is when moving from an nvidia chipset to a intel chipset. i can vouch for moving from one nvidia chipset to a completely different one, and i've read a lot of people say they migrated on intel chipsets too. if it doesn't just get recognized as an array when you enable SATA RAID in the BIOS then maybe you lost data on the drives somewhere during the transfer (it can take less magnetic energy than you think).

a NSD message just means that a bootsector wasn't found on the drive(s), which makes sense considering the drives don't have any data that can be used outside of the array.

first of all it doesn't matter what order the disks are in. second, all you should have to do is enable RAID in the BIOS for the proper SATA ports, save and reboot and when the intel RAID screen comes up it should detect the RAID array. the only time this has not worked for me is when moving from an nvidia chipset to a intel chipset. i can vouch for moving from one nvidia chipset to a completely different one, and i've read a lot of people say they did it on their intels too. if it doesn't just get recognized as an array when you enable SATA RAID in the BIOS then maybe you lost data on the drives somewhere during the transfer (it can take less magnetic energy than you think).

a NSD message just means that a bootsector wasn't found on the drive(s).

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So the configuration that gives me NSD is the wrong one and I should swap the drives? That was my hunch at least...

According to several colleagues here (IT department) the order is important when striping, not when mirroring.